[Bioc-devel] GenomicRanges::cbind() problem

[Michael Lawrence]

I think this was fixed in S4Vectors a couple of days ago but I forgot
to bump the version (just did). Sorry.

On Tue, Sep 12, 2017 at 12:06 AM, Robert Castelo <robert.castelo at upf.edu> wrote:
> dear GenomicRanges developers,
>
> my package qpgraph is breaking in devel due to the following behavior of
> GenomicRanges:
>
> library(GenomicRanges)
> gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))
> mcols(gr)
> DataFrame with 10 rows and 0 columns
> mcols(gr) <- cbind(mcols(gr), DataFrame(test=rep(1, 10)))
> gr
> GRanges object with 10 ranges and 1 metadata column:
>        seqnames    ranges strand |       dfs
>           <Rle> <IRanges>  <Rle> | <numeric>
>    [1]        1  [ 1,  1]      * |         1
>    [2]        1  [ 2,  2]      * |         1
>    [3]        1  [ 3,  3]      * |         1
>    [4]        1  [ 4,  4]      * |         1
>    [5]        1  [ 5,  5]      * |         1
>    [6]        1  [ 6,  6]      * |         1
>    [7]        1  [ 7,  7]      * |         1
>    [8]        1  [ 8,  8]      * |         1
>    [9]        1  [ 9,  9]      * |         1
>   [10]        1  [10, 10]      * |         1
>   -------
>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> notice that the metadata column i've added should be called 'test' and it is
> called 'dfs' instead. this does not happen in release:
>
> library(GenomicRanges)
> gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))
> mcols(gr)
> DataFrame with 10 rows and 0 columns
> mcols(gr) <- cbind(mcols(gr), DataFrame(test=rep(1, 10)))
> gr
> GRanges object with 10 ranges and 1 metadata column:
>        seqnames    ranges strand |      test
>           <Rle> <IRanges>  <Rle> | <numeric>
>    [1]        1  [ 1,  1]      * |         1
>    [2]        1  [ 2,  2]      * |         1
>    [3]        1  [ 3,  3]      * |         1
>    [4]        1  [ 4,  4]      * |         1
>    [5]        1  [ 5,  5]      * |         1
>    [6]        1  [ 6,  6]      * |         1
>    [7]        1  [ 7,  7]      * |         1
>    [8]        1  [ 8,  8]      * |         1
>    [9]        1  [ 9,  9]      * |         1
>   [10]        1  [10, 10]      * |         1
>   -------
>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> i guess that if doing 'cbind()' with an empty 'DataFrame' is not allowed
> anymore, the correct behavior should be giving an error but renaming the
> column seems bogus to me.
>
> please find below my session information bits for both, devel and release.
>
> cheers,
>
> robert.
>
> devel sessionInfo():
>
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> Matrix products: default
> BLAS: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRblas.so
> LAPACK: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
>  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] GenomicRanges_1.29.13 GenomeInfoDb_1.13.4 IRanges_2.11.15
> [4] S4Vectors_0.15.7      BiocGenerics_0.23.1 colorout_1.1-2
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.23.0         compiler_3.4.0 tools_3.4.0
> [4] XVector_0.17.1          GenomeInfoDbData_0.99.1 RCurl_1.95-4.8
> [7] bitops_1.0-6
>
> release sessionInfo():
>
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> Matrix products: default
> BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so
> LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
>  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 IRanges_2.10.3
> [4] S4Vectors_0.14.3     BiocGenerics_0.22.0 colorout_1.1-2
>
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.22.0         compiler_3.4.0 XVector_0.16.0
> [4] GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 bitops_1.0-6
>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>
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